When a crystal absorbs a photon, that energy becomes part of the
crystal. When that same crystal releases a photon, that photon is
taking energy away from the crystal.
The Stokes Shift is a measure of the difference in wavelength
(and thus energy) of photons absorbed by a crystal and then
immediately re-emitted by that same crystal. The energy shift
between the two photons is an indication of how much energy has
been permanently absorbed by the crystal in the form of heat.